3kyd

Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic


Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating the activities of those targets in various ways. Three types of evolutionarily conserved enzymes — E1 activating enzymes, E2 conjugating enzymes and E3 ligase enzymes — act sequentially through parallel yet distinct pathways to conjugate ubiquitin and Ubl proteins, such as SUMO and NEDD8, to their targets. The E1 enzyme uses the adenosine triphosphate (ATP) and magnesium to adenylate the C-terminal Ub/Ubl glycine, releasing pyrophosphate and resulting in adenosine monophosphate (AMP). A non-hydrolysable mimic of the acyl adenylate intermediate (AMSN) and mimic of the tetrahedral intermediate (AVSN) were constructed. In both these compounds the atom of phosphorus is replaced by sulfur (colored yellow ).

The structural alignment of the crystal structures for human SUMO E1 in complex with SUMO adenylate (AMSN) and tetrahedral intermediate (AVSN) analogues revealed opened conformation (SUMO1 in orange, SAE1 colored in blue , and other domains in darkviolet ) and closed conformation ( SUMO1 in yellow , SAE1 colored in cyan , and other domains in magenta ), respectively. In the open conformation (3kyc) the distance between Cys domain (including Cys173) and mimic of the acyl adenylate intermediate AMSN is very long, while in the closed conformation (3kyd), the catalytic Cys173 is posioned near AVSN and SUMO1, so the overall structure revealed dramatic rearrangement. This large conformational change forms the E1~SUMO1-AVSN tetrahedral intermediate analogue. 

For better understanding of the difference between these two conformations you can see this morph (generated by using POLYVIEW-3D: http://polyview.cchmc.org/polyview3d.html; reload/refresh this page to restart this movie). Of note, in contrast to the previous figure, the same domains of these two structures (3kyc and 3kyd) are colored in the same colors ( SUMO1 in yellow, <font color='blue'>SAE1 colored in blue and <font color='darkviolet'>other domains in darkviolet ). The catalytic Cys173 is shown in the spacefill representation and colored green, AMSN (or AVSN) are shown in the spacefill representation and colored in CPK colors.

About this Structure
3KYD is a 3 chains structure with sequences from Homo sapiens. Full crystallographic information is available from OCA.

Reference
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